Mercurial > repos > ecology > hirondelle_crim
changeset 0:afede0916f0a draft
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/ogc_api_processes_wrapper commit 89c188931ba43399013ebc741bc14365e53d418a
| author | ecology |
|---|---|
| date | Fri, 07 Jun 2024 11:37:33 +0000 |
| parents | |
| children | 52baddd15640 |
| files | crim_project_ogc_api_processes.xml macros.xml ogc_api_processes_wrapper.R test-data/crim_test_input.json |
| diffstat | 4 files changed, 511 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crim_project_ogc_api_processes.xml Fri Jun 07 11:37:33 2024 +0000 @@ -0,0 +1,221 @@ +<tool id="hirondelle_crim" name="Hirondelle CRIM OGC API Processes" version="0.1.0" profile="22.05"> + <description>executes remote processes.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/ogc_api_processes_wrapper.R' + --outputData '$output_data' +]]></command> + <configfiles> + <inputs name="inputs" filename="inputs.json" data_style="paths"/> + </configfiles> + <inputs> + <conditional name="conditional_process"> + <param name="select_process" type="select" label="Select process"> + <option value="algae-usecase-workflow-copernicus">algae-usecase-workflow-copernicus: Algae bloom for water quality assessment on Sentinel-2 imagery offered by Copernicus platform.</option> + <option value="algae-usecase-workflow-copernicus-process">algae-usecase-workflow-copernicus-process: Processing on Sentinel-2 bands to evaluate algae bloom.</option> + <option value="algae-usecase-workflow-earth-search">algae-usecase-workflow-earth-search: Algae bloom for water quality assessment on Sentinel-2 L2A imagery offered by Earth-Search platform.</option> + <option value="algae-usecase-workflow-earth-search-process">algae-usecase-workflow-earth-search-process: Processing on Sentinel-2 L2A bands to evaluate algae bloom.</option> + <option value="calculate-band">calculate-band: Performs a calculation with bands.</option> + <option value="download-band-sentinel2-product-safe">download-band-sentinel2-product-safe: Downloads Copernicus products.</option> + <option value="download-band-sentinel2-stac-item">download-band-sentinel2-stac-item: Downloads Sentinel-2 GeoTiff from STAC Item.</option> + <option value="EchoProcess">EchoProcess</option> + <option value="file_index_selector">file_index_selector: File Index Selector</option> + <option value="file2string_array">file2string_array: File to String-Array</option> + <option value="jsonarray2netcdf">jsonarray2netcdf: JSON array to NetCDF</option> + <option value="metalink2netcdf">metalink2netcdf: Metalink to NetCDF</option> + <option value="ogc-tb16-land-cover-mapping">ogc-tb16-land-cover-mapping: OGC Testbed-16 Pixel-Wise Classifier for Land Cover Mapping</option> + <option value="plot-image">plot-image: Plots an image with colors.</option> + <option value="reproject-image">reproject-image: Performs image reprojection.</option> + <option value="select-products-sentinel2">select-products-sentinel2: Searches the specified catalog for Sentinel-2 products matching filtering criteria.</option> + </param> + <when value="algae-usecase-workflow-copernicus"> + <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="date" label="date" optional="false" value="" type="text"/> + <param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="aoi" label="aoi" optional="false" value="" type="data" format="txt"/> + <param name="collection" label="collection" optional="false" value="" type="text"/> + <param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> + </when> + <when value="algae-usecase-workflow-copernicus-process"> + <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="product_url" label="product_url" optional="false" value="" type="text"/> + </when> + <when value="algae-usecase-workflow-earth-search"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="date_Array_text" label="date" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="toi_Array_text" label="toi" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="aoi" label="aoi" optional="false" value="" help="Polygon defining the area of interest." type="data" format="txt"/> + <param name="collection" label="collection" optional="false" value="" type="text"/> + <param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> + </when> + <when value="algae-usecase-workflow-earth-search-process"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="product_url" label="product_url" optional="false" value="" help="The STAC Item should contain Assets with Sentinel-2 product bands." type="text"/> + </when> + <when value="calculate-band"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="name" label="name" optional="false" value="" help="Name to apply for the output GeoTiff file." type="text"/> + <param name="calc" label="calc" optional="false" value="" help="Calculation to perform with band references." type="text"/> + <param name="band_a" label="band_a" optional="false" value="" type="text"/> + <param name="band_b" label="band_b" optional="false" value="" type="text"/> + <param name="band_c" label="band_c" optional="false" value="" type="text"/> + <param name="band_d" label="band_d" optional="false" value="" type="text"/> + <param name="band_e" label="band_e" optional="false" value="" type="text"/> + <param name="band_f" label="band_f" optional="false" value="" type="text"/> + <param name="band_g" label="band_g" optional="false" value="" type="text"/> + <param name="band_h" label="band_h" optional="false" value="" type="text"/> + <param name="band_i" label="band_i" optional="false" value="" type="text"/> + <param name="band_j" label="band_j" optional="false" value="" type="text"/> + <param name="band_k" label="band_k" optional="false" value="" type="text"/> + <param name="band_l" label="band_l" optional="false" value="" type="text"/> + <param name="band_m" label="band_m" optional="false" value="" type="text"/> + <param name="band_n" label="band_n" optional="false" value="" type="text"/> + <param name="band_o" label="band_o" optional="false" value="" type="text"/> + <param name="band_p" label="band_p" optional="false" value="" type="text"/> + <param name="band_q" label="band_q" optional="false" value="" type="text"/> + <param name="band_r" label="band_r" optional="false" value="" type="text"/> + <param name="band_s" label="band_s" optional="false" value="" type="text"/> + <param name="band_t" label="band_t" optional="false" value="" type="text"/> + <param name="band_u" label="band_u" optional="false" value="" type="text"/> + <param name="band_v" label="band_v" optional="false" value="" type="text"/> + <param name="band_w" label="band_w" optional="false" value="" type="text"/> + <param name="band_x" label="band_x" optional="false" value="" type="text"/> + <param name="band_y" label="band_y" optional="false" value="" type="text"/> + <param name="band_z" label="band_z" optional="false" value="" type="text"/> + </when> + <when value="download-band-sentinel2-product-safe"> + <param name="user_credentials" label="user_credentials" optional="false" type="data" format="json"/> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="product_url" label="product_url" optional="false" value="" type="text"/> + <param name="resolution_Array_text" label="resolution" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="band" label="band" optional="false" value="" type="select"> + <option value="B01">B01</option> + <option value="B02">B02</option> + <option value="B03">B03</option> + <option value="B04">B04</option> + <option value="B05">B05</option> + <option value="B06">B06</option> + <option value="B07">B07</option> + <option value="B08">B08</option> + <option value="B8A">B8A</option> + <option value="B09">B09</option> + <option value="B11">B11</option> + <option value="B12">B12</option> + <option value="AOT">AOT</option> + <option value="SCL">SCL</option> + <option value="TCI">TCI</option> + <option value="WVP">WVP</option> + </param> + <param name="debug_Array_boolean" label="debug" value="" help="Please provide comma-seperated values of type boolean here." type="text"/> + </when> + <when value="download-band-sentinel2-stac-item"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="product_url" label="product_url" optional="false" value="" type="text"/> + <param name="band" label="band" optional="false" value="" type="select"> + <option value="B01">B01</option> + <option value="B02">B02</option> + <option value="B03">B03</option> + <option value="B04">B04</option> + <option value="B05">B05</option> + <option value="B06">B06</option> + <option value="B07">B07</option> + <option value="B08">B08</option> + <option value="B8A">B8A</option> + <option value="B09">B09</option> + <option value="B11">B11</option> + <option value="B12">B12</option> + <option value="AOT">AOT</option> + <option value="SCL">SCL</option> + <option value="TCI">TCI</option> + <option value="WVP">WVP</option> + </param> + </when> + <when value="EchoProcess"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="stringInput" label="stringInput" optional="false" value="" type="select"> + <option value="Value1">Value1</option> + <option value="Value2">Value2</option> + <option value="Value3">Value3</option> + </param> + <param name="measureInput" label="measureInput" optional="false" help="This is an example of a NUMERIC literal with an associated unit of measure." type="text"/> + <param name="dateInput" label="dateInput" optional="false" value="" help="This is an example of a DATE literal input." type="text"/> + <param name="doubleInput" label="doubleInput" optional="false" value="" help="This is an example of a DOUBLE literal input that is bounded between a value greater than 0 and 10. The default value is 5." type="float"/> + <param name="arrayInput_Array_integer" label="arrayInput" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="complexObjectInput" label="complexObjectInput" optional="false" help="This is an example of a complex object input." type="text"/> + <param name="geometryInput" label="geometryInput" optional="false" value="" help="This is an example of a geometry input. In this case the geometry can be expressed as a GML of GeoJSON geometry." type="text"/> + <param name="boundingBoxInput" label="boundingBoxInput" optional="false" help="This is an example of an image input. In this case, the input is an array of up to 150 images that might, for example, be a set of tiles. The oneOf[] conditional is used to indicate the acceptable image content types; GeoTIFF and JPEG 2000 in this case. Each input image in the input array can be included inline in the execute request as a base64-encoded string or referenced using the link.yaml schema. The use of a base64-encoded string is implied by the specification and does not need to be specified in the definition of the input." type="data" format="txt"/> + <param name="imagesInput" label="imagesInput" optional="false" help="This is an example of an image input. In this case, the input is an array of up to 150 images that might, for example, be a set of tiles. The oneOf[] conditional is used to indicate the acceptable image content types; GeoTIFF and JPEG 2000 in this case. Each input image in the input array can be included inline in the execute request as a base64-encoded string or referenced using the link.yaml schema. The use of a base64-encoded string is implied by the specification and does not need to be specified in the definition of the input." type="data" format="txt"/> + <param name="featureCollectionInput" label="featureCollectionInput" optional="false" help="This is an example of an input that is a feature collection that can be encoded in one of three ways. As a GeoJSON feature collection, as a GML feature collection retrieved from a WFS or as a KML document." type="text"/> + </when> + <when value="file_index_selector"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="files" label="files" optional="false" type="data" format="txt"/> + <param name="index" label="index" optional="false" value="" type="integer"/> + </when> + <when value="file2string_array"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="input" label="input" optional="false" value="" type="data" format="txt"/> + </when> + <when value="jsonarray2netcdf"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="input" label="input" optional="false" value="" help="JSON file formed of an array of file URIs, each representing NetCDF contents." type="text"/> + </when> + <when value="metalink2netcdf"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="input" label="input" optional="false" type="text"/> + <param name="index" label="index" optional="false" value="" help="Index of the MetaLink file to extract. This index is 1-based." type="integer"/> + </when> + <when value="ogc-tb16-land-cover-mapping"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="raster_file" label="raster_file" optional="false" help="Input raster onto which to run object classification. Either a Sentinel-2 SAFE ZIP or a RBG-NIR GeoTiff." type="data" format="txt"/> + <param name="raster_bands_Array_integer" label="raster_bands" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="raster_mean_Array_float" label="raster_mean" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> + <param name="raster_std_Array_float" label="raster_std" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> + <param name="patch_size_Array_integer" label="patch_size" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="batch_size_Array_integer" label="batch_size" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="device_Array_text" label="device" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + </when> + <when value="plot-image"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="input_image" label="input_image" optional="false" value="" help="Image to map with the colors bins." type="data" format="txt"/> + <param name="color_scale" label="color_scale" optional="false" value="" help="JSON-like array with each item being an array of 2 elements, the first for the bin scale value and the second for the RGB color. Each RGB value can be either a [0-1] floating point or a [0-255] integer. Example: '[ [0, [0,0,0]], [20, [0,0,255]], [50, [255,100,0]] ]'" type="text"/> + <param name="output_name_Array_text" label="output_name" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="plot_name_Array_text" label="plot_name" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="plot_title_Array_text" label="plot_title" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + </when> + <when value="reproject-image"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="input_image" label="input_image" optional="false" type="data" format="txt"/> + <param name="output_dimensions_Array_integer" label="output_dimensions" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="output_resolution_Array_integer" label="output_resolution" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="output_name" label="output_name" optional="false" value="" help="Name to apply for the output GeoTiff file." type="text"/> + </when> + <when value="select-products-sentinel2"> + <param name="cookie" label="cookie" optional="false" value="" type="text"/> + <param name="date_Array_text" label="date" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="delta_Array_integer" label="delta" optional="false" value="" help="Please provide comma-seperated values of type integer here." type="text"/> + <param name="toi_Array_text" label="toi" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="aoi" label="aoi" optional="false" value="" help="Polygon defining the area of interest." type="data" format="txt"/> + <param name="collection" label="collection" optional="false" value="" type="text"/> + <param name="product_level_Array_text" label="product_level" optional="false" value="" help="Please provide comma-seperated values of type text here." type="text"/> + <param name="catalog" label="catalog" optional="false" value="" type="select"> + <option value="copernicus">copernicus</option> + <option value="earth-search">earth-search</option> + </param> + <param name="cloud_cover_Array_float" label="cloud_cover" optional="false" value="" help="Please provide comma-seperated values of type float here." type="text"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_data" format="txt" label="$select_process"/> + </outputs> + <expand macro="tests"/> + <help>Use the dropdown menu at the top to select the process and then complete the corresponding from, which is different for every process.</help> + <expand macro="citations"/> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Jun 07 11:37:33 2024 +0000 @@ -0,0 +1,47 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.3.1">r-base</requirement> + <requirement type="package" version="1.20.4">r-getopt</requirement> + <requirement type="package" version="0.2.3">r-httr2</requirement> + <requirement type="package" version="1.8.7">r-jsonlite</requirement> + </requirements> + </xml> + <xml name="out_options"> + <option value="uint8">uint8</option> + <option value="uint16">uint16</option> + <option value="int16">int16</option> + <option value="int32">int32</option> + <option value="float">float</option> + <option value="double">double</option> + </xml> + <xml name="format_options"> + <option value="image/tiff">image/tiff</option> + <option value="image/jpeg">image/jpeg</option> + <option value="image/png">image/png</option> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex">@Manual{httr2, title = {httr2: Perform HTTP Requests and Process the Responses}, author = {Hadley Wickham}, year = {2023}, note = {R package version 1.0.0, https://github.com/r-lib/httr2}, url = {https://httr2.r-lib.org},}</citation> + <citation type="doi">10.48550/arXiv.1403.2805</citation> + </citations> + </xml> + <xml name="help"> + <help>This tool is a wrapper for OGC API Processes (OTB) coming from the Zoo Project (https://zoo-project.github.io/docs/intro.html) and was created using the OGC-API-Process2Galaxy tool (https://github.com/AquaINFRA/OGC-API-Process2Galaxy). Check the README in the repository for more information.</help> + </xml> + <xml name="tests"> + <tests> + <test expect_failure="true"> + <param name="select_process" value="download-band-sentinel2-product-safe"/> + <param name="user_credentials" value="crim_test_input.json"/> + <param name="cookie" value=""/> + <param name="product_url" value="s3:///eodata/Sentinel-2/MSI/L2A/2019/07/01/S2A_MSIL2A_20190701T110621_N0212_R137_T29SPC_20190701T120906.SAFE"/> + <param name="resolution_Array_text" value="10m"/> + <param name="band" value="B04"/> + <assert_stderr> + <has_text text="HTTP 401 Unauthorized"/> + </assert_stderr> + </test> + </tests> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ogc_api_processes_wrapper.R Fri Jun 07 11:37:33 2024 +0000 @@ -0,0 +1,239 @@ +library("httr2") +library("jsonlite") +library("getopt") + +cat("start generic wrapper service \n") + +getParameters <- function(){ + con <- file("inputs.json", "r") + lines <- readLines(con) + close(con) + + json_string <- paste(lines, collapse = "\n") + json_data <- fromJSON(json_string) + return(json_data$conditional_process) +} + +parseResponseBody <- function(body) { + hex <- c(body) + intValues <- as.integer(hex) + rawVector <- as.raw(intValues) + readableOutput <- rawToChar(rawVector) + jsonObject <- jsonlite::fromJSON(readableOutput) + return(jsonObject) +} + +getOutputs <- function(inputs, output, server) { + url <- paste(paste(server, "/processes/", sep = ""), inputs$select_process, sep = "") + request <- request(url) + response <- req_perform(request) + responseBody <- parseResponseBody(response$body) + outputs <- list() + + for (x in 1:length(responseBody$outputs)) { + outputformatName <- paste(names(responseBody$outputs[x]), "_outformat", sep="") + output_item <- list() + + for (p in names(inputs)) { + if(p == outputformatName){ + format <- list("mediaType" = inputs[[outputformatName]]) + output_item$format <- format + } + } + output_item$transmissionMode <- "reference" + outputs[[x]] <- output_item + } + + names(outputs) <- names(responseBody$outputs) + return(outputs) +} + +executeProcess <- function(url, process, requestBodyData, cookie) { + url <- paste(paste(paste(url, "processes/", sep = ""), process, sep = ""), "/execution", sep = "") + requestBodyData$inputs$cookie <- NULL + requestBodyData$inputs$select_process <- NULL + + requestBodyData$inputs$s3_access_key <- requestBodyData$inputs$user_credentials$s3_access_key + requestBodyData$inputs$s3_secret_key <- requestBodyData$inputs$user_credentials$s3_secret_key + requestBodyData$inputs$user_credentials <- NULL + + body <- list() + body$inputs <- requestBodyData$inputs + body$mode <- "async" + body$response <- "document" + + response <- request(url) %>% + req_headers( + "Accept" = "application/json", + "Content-Type" = "application/json", + "Cookie" = cookie + ) %>% + req_body_json(body) %>% + req_perform() + + cat("\n Process executed") + cat("\n status: ", response$status_code) + cat("\n jobID: ", parseResponseBody(response$body)$jobID, "\n") + + jobID <- parseResponseBody(response$body)$jobID + + return(jobID) +} + +checkJobStatus <- function(server, process, jobID, cookie) { + url <- paste0(server, "processes/", process, "/jobs/", jobID) + response <- request(url) %>% + req_headers( + "Cookie" = cookie + ) %>% + req_perform() + jobStatus <- parseResponseBody(response$body)$status + jobProgress <- parseResponseBody(response$body)$progress + return(jobStatus) +} + +getStatusCode <- function(server, process, jobID, cookie) { + url <- paste0(server, "processes/", process, "/jobs/", jobID) + response <- request(url) %>% + req_headers( + "Cookie" = cookie + ) %>% + req_perform() + status_code <- response$status_code + return(status_code) +} + +getResult <- function (server, process, jobID, cookie) { + response <- request(paste0(server, "processes/", process, "/jobs/", jobID, "/results")) %>% + req_headers( + "Cookie" = cookie + ) %>% + req_perform() + return(response) +} + +retrieveResults <- function(server, process, jobID, outputData, cookie) { + status_code <- getStatusCode(server, process, jobID, cookie) + if(status_code == 200){ + status <- "running" + while(status == "running"){ + jobStatus <- checkJobStatus(server, process, jobID, cookie) + print(jobStatus) + if (jobStatus == "succeeded") { + status <- jobStatus + result <- getResult(server, process, jobID, cookie) + if (result$status_code == 200) { + resultBody <- parseResponseBody(result$body) + urls <- unname(unlist(lapply(resultBody, function(x) x$href))) + urls_with_newline <- paste(urls, collapse = "\n") + con <- file(outputData, "w") + writeLines(urls_with_newline, con = con) + close(con) + } + } else if (jobStatus == "failed") { + status <- jobStatus + } + Sys.sleep(3) + } + cat("\n done \n") + } else if (status_code1 == 400) { + print("A query parameter has an invalid value.") + } else if (status_code1 == 404) { + print("The requested URI was not found.") + } else if (status_code1 == 500) { + print("The requested URI was not found.") + } else { + print(paste("HTTP", status_code1, "Error:", resp1$status_message)) + } +} + +is_url <- function(x) { + grepl("^https?://", x) +} + +server <- "https://hirondelle.crim.ca/weaver/" + +print("--> Retrieve parameters") +inputParameters <- getParameters() +print("--> Parameters retrieved") + +args <- commandArgs(trailingOnly = TRUE) +outputLocation <- args[2] + +print("--> Retrieve outputs") +outputs <- getOutputs(inputParameters, outputLocation, server) +print("--> Outputs retrieved") + +print("--> Parse inputs") +convertedKeys <- c() +for (key in names(inputParameters)) { + if (is.character(inputParameters[[key]]) && (endsWith(inputParameters[[key]], ".dat") || endsWith(inputParameters[[key]], ".txt"))) { + con <- file(inputParameters[[key]], "r") + url_list <- list() + #while (length(line <- readLines(con, n = 1)) > 0) { + # if (is_url(line)) { + # url_list <- c(url_list, list(list(href = trimws(line)))) + # } + #} + con <- file(inputParameters[[key]], "r") + lines <- readLines(con) + close(con) + json_string <- paste(lines, collapse = "\n") + json_data <- fromJSON(json_string) + + inputParameters[[key]] <- json_data + convertedKeys <- append(convertedKeys, key) + } + else if (grepl("_Array_", key)) { + keyParts <- strsplit(key, split = "_")[[1]] + type <- keyParts[length(keyParts)] + values <- inputParameters[[key]] + value_list <- strsplit(values, split = ",") + + convertedValues <- c() + + for (value in value_list) { + if(type == "integer") { + value <- as.integer(value) + } else if (type == "numeric") { + value <- as.numeric(balue) + } else if (type == "character") { + value <- as.character(value) + } + convertedValues <- append(convertedValues, value) + + convertedKey <- "" + for (part in keyParts) { + if(part == "Array") { + break + } + convertedKey <- paste(convertedKey, paste(part, "_", sep=""), sep="") + } + convertedKey <- substr(convertedKey, 1, nchar(convertedKey)-1) +} + + inputParameters[[key]] <- convertedValues + convertedKeys <- append(convertedKeys, convertedKey) + } else { + convertedKeys <- append(convertedKeys, key) + } +} + +names(inputParameters) <- convertedKeys +print("--> Inputs parsed") + +print("--> Prepare process execution") +jsonData <- list( + "inputs" = inputParameters, + "outputs" = outputs +) + +cookie <- inputParameters$cookie + +print("--> Execute process") +jobID <- executeProcess(server, inputParameters$select_process, jsonData, cookie) +print("--> Process executed") + +print("--> Retrieve results") +retrieveResults(server, inputParameters$select_process, jobID, outputLocation, cookie) +print("--> Results retrieved") \ No newline at end of file